Check simulation sim_4.5
Alessio Crippa
12 February, 2019
Dynamic report for checking simulation design (4.5)
True mean Progression Free Time (PFT)
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 7.11 7.11 5.40 7.11 5.40
---+ 7.11 7.11 5.40 7.11 17.01
--+- 7.11 7.11 5.40 7.11 5.40
--++ 7.11 7.11 5.40 7.11 17.01
-+-- 7.11 7.11 17.01 7.11 5.40
-+-+ 7.11 7.11 17.01 7.11 17.01
-++- 7.11 7.11 17.01 7.11 5.40
-+++ 7.11 7.11 17.01 7.11 17.01
+--- 7.11 7.11 5.40 7.11 5.40
+--+ 7.11 7.11 5.40 7.11 17.01
+-+- 7.11 7.11 5.40 7.11 5.40
+-++ 7.11 7.11 5.40 7.11 17.01
++-- 7.11 7.11 17.01 7.11 5.40
++-+ 7.11 7.11 17.01 7.11 17.01
+++- 7.11 7.11 17.01 7.11 5.40Graduation output
$superiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 0 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 0 0 0
DRD+ 0 0 1 0 0
TEfus+ 0 0 0 0 1
$inferiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 0 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 0 0 0
DRD+ 0 0 0 0 0
TEfus+ 0 1 0 0 0Final probability of superioriry by signatures and biomarkers subtypes
$p_sign
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0.03 0.02 0.23 0.01 0.19
TP53- & AR- 0.38 0.12 0.98 0.35 0.36
TP53+ 0.10 0.18 0.07 0.07 0.34
DRD+ 0.11 0.09 0.80 0.06 0.08
TEfus+ 0.01 0.00 0.04 0.00 0.48
$p_type
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 0.06 0.29 0.08 0.42 0.13
---+ 0.34 0.07 0.29 0.16 0.64
--+- 0.78 0.91 0.33 0.89 0.74
--++ 0.20 0.14 0.09 0.16 0.82
-+-- 0.78 0.71 1.00 0.75 0.32
-+-+ 0.52 0.19 0.84 0.50 0.38
-++- 0.78 0.73 0.76 0.62 0.62
-+++ 0.08 0.15 0.18 0.18 0.17
+--- 0.50 0.29 0.20 0.34 0.13
+--+ 0.26 0.18 0.20 0.31 0.77
+-+- 0.46 0.50 0.44 0.38 0.38
+-++ 0.02 0.05 0.01 0.03 0.36
++-- 0.08 0.09 0.44 0.06 0.07
++-+ 0.15 0.15 0.20 0.10 0.40
+++- 0.42 0.48 0.38 0.32 0.32
Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 87 52 80 18 79 31
---+ 17 20 8 4 12 6
--+- 43 38 42 22 32 32
--++ 51 13 8 15 18 7
-+-- 17 13 13 12 12 8
-+-+ 22 10 2 4 10 0
-++- 4 1 0 1 5 3
-+++ 3 1 2 1 3 0
+--- 10 6 5 4 10 7
+--+ 12 10 2 3 12 3
+-+- 4 2 2 0 2 1
+-++ 21 5 2 4 5 3
++-- 9 11 4 1 7 2
++-+ 5 2 1 0 3 1
+++- 2 2 2 1 5 5 Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 307 186 173 90 215 109
TP53- & AR- 143 95 103 38 113 45
TP53+ 128 62 58 44 70 51
DRD+ 62 40 24 20 45 19
TEfus+ 131 61 25 31 63 20
Number of events, PT, and rate by subtype (over time)
Number of events, PT, and rate by signature (over time)
Analysis of final simulated results
Sample of 10 rows:
id trt trt2 line subtype delta month0 time_m all TP53- & AR- TP53+ DRD+ TEfus+
448 411 Carboplatin Carboplatin 1 --+- 1 13 3.2212011 1 0 1 0 0
139 130 Enzalutamide Enzalutamide 1 ---- 1 4 2.6587299 1 1 0 0 0
266 249 Enzalutamide Enzalutamide 1 --+- 1 8 5.4700406 1 0 1 0 0
769 692 Control Enzalutamide 1 ---- 1 23 1.2719507 1 1 0 0 0
166 155 Control Abiraterone 1 -+-- 1 5 6.6289854 1 1 0 1 0
286 269 Docetaxel Docetaxel 1 +-+- 1 8 0.6937390 1 0 1 0 0
588 531 Cabazitaxel Cabazitaxel 1 ---- 1 17 8.0275362 1 1 0 0 0
1079 966 Control Docetaxel 1 +-++ 0 32 4.0000000 1 0 1 0 1
503 452 Control Enzalutamide 1 ---- 1 15 3.5181482 1 1 0 0 0
648 584 Enzalutamide Enzalutamide 1 -+-- 1 19 0.8915835 1 1 0 1 0Descriptives
Mean number of progressions and follow-up time:
$all
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 261 2213. 0.118
2 Enzalutamide 166 1101. 0.151
3 Abiraterone 157 1049. 0.150
4 Carboplatin 86 689. 0.125
5 Cabazitaxel 200 1395. 0.143
6 Docetaxel 104 785. 0.132
$`TP53- & AR-`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 129 1015. 0.127
2 Enzalutamide 89 606. 0.147
3 Abiraterone 96 638. 0.150
4 Carboplatin 36 442. 0.0814
5 Cabazitaxel 101 760. 0.133
6 Docetaxel 43 274. 0.157
$`TP53+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 107 864. 0.124
2 Enzalutamide 55 332. 0.166
3 Abiraterone 50 355. 0.141
4 Carboplatin 43 186. 0.231
5 Cabazitaxel 69 432. 0.160
6 Docetaxel 47 373. 0.126
$`DRD+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 50 465. 0.108
2 Enzalutamide 39 278. 0.140
3 Abiraterone 26 153. 0.170
4 Carboplatin 17 381. 0.0446
5 Cabazitaxel 46 288. 0.160
6 Docetaxel 21 93.4 0.225
$`TEfus+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 99 1014. 0.0976
2 Enzalutamide 53 350. 0.152
3 Abiraterone 27 94.1 0.287
4 Carboplatin 30 194. 0.155
5 Cabazitaxel 57 361. 0.158
6 Docetaxel 20 332. 0.0602
Kaplan-Meier results:
$all
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 343 261 5.72 4.83 6.68
trt=Enzalutamide 203 166 4.46 3.72 5.50
trt=Abiraterone 193 157 4.46 3.78 5.49
trt=Carboplatin 100 86 4.36 3.68 6.36
trt=Cabazitaxel 247 200 5.02 4.24 5.74
trt=Docetaxel 126 104 4.82 3.61 7.99
$`TP53- & AR-`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 161 129 5.22 4.19 7.00
trt=Enzalutamide 103 89 4.12 3.17 6.05
trt=Abiraterone 114 96 4.44 3.56 5.49
trt=Carboplatin 43 36 9.23 3.96 15.60
trt=Cabazitaxel 133 101 5.02 3.97 5.82
trt=Docetaxel 53 43 4.79 3.57 8.42
$`TP53+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 145 107 5.44 4.54 6.68
trt=Enzalutamide 70 55 4.63 3.66 6.27
trt=Abiraterone 66 50 5.57 3.69 7.88
trt=Carboplatin 47 43 3.77 2.84 5.49
trt=Cabazitaxel 79 69 4.91 3.74 6.59
trt=Docetaxel 57 47 6.00 3.34 9.18
$`DRD+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 69 50 5.62 4.01 9.72
trt=Enzalutamide 47 39 4.12 2.64 7.48
trt=Abiraterone 30 26 3.36 2.47 7.33
trt=Carboplatin 20 17 18.70 12.26 31.80
trt=Cabazitaxel 52 46 4.90 3.85 6.88
trt=Docetaxel 22 21 2.79 1.89 6.29
$`TEfus+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 145 99 7.00 5.62 9.36
trt=Enzalutamide 68 53 4.64 2.64 6.26
trt=Abiraterone 27 27 2.53 1.80 4.46
trt=Carboplatin 35 30 4.36 3.04 7.86
trt=Cabazitaxel 69 57 4.82 3.89 7.88
trt=Docetaxel 22 20 12.55 12.00 21.18
